Most print editions count only spoken lines in numbering lines within a scene, and start afresh with each scene. (MLA uses Hindu-Arabic numerals exclusively, separated by periods, for citations by act and scene or by act, scene, and line.) The line numbering in various editions will be consistent in the case of an all-verse play, such as Richard II, but will vary in scenes that contain some prose, since different column widths and typefaces will determine where line breaks fall in prose. Even verse passages that follow prose ones within the same scene will thus be line-numbered differently from one edition to the next.
The only entirely reliable system for citing loci in Shakespeare’s plays involves specifying an early printing (Q2 or F, say, for the second quarto or [first] folio text of Hamlet) and a line number that counts all the printed lines in that printed text from first to last, including stage directions and everything—what is called TLN (Through Line Numbering).
In dealing with the early printings, which serious Shakespeareans in both academe and the theater tend to do, be prepared for very minimal stage directions. Also, the quartos printed in Shakespeare’s lifetime generally did not divide a play at all; it was only the posthumous 1623 first folio that divided the plays into five acts each and in some cases subdivided each act into numbered scenes as well. Notations regarding where each scene is set, plus lists of Dramatis Personae, were contributed only by later editors, starting with Nicholas Rowe.
On-line access to exact transcriptions of the early printings, with TLN, can be had via the Internet Shakespeare Editions site, hosted by the University of Victoria (British Columbia, Canada). Complete facsimile images of many of the early printings are also available there.